MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics
MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics
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DOI：
10.3390/metabo10050186
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发表时间：
2020-05-01
期刊：
影响因子：
4.1
通讯作者：
Xia, Jianguo
中科院分区：
文献类型：
--
作者：
Pang, Zhiqiang;Chong, Jasmine;Xia, Jianguo
液相色谱结合高分辨率质谱平台越来越多地用于全面测量系统生物学和复杂疾病中的代谢组学变化。在过去的十年中，已经开发了几个强大的计算管道，用于光谱处理，注释和分析。然而，在参数设置、计算效率、批量效应和功能解释方面仍然存在重大障碍。在这里，我们介绍了MetaboAnalystR 3.0，这是一个显著改进的管道，具有三个关键的新功能：（1）高效的峰拾取参数优化;（2）自动批次效应校正;（3）更准确的途径活性预测。我们的基准研究表明，与其他成熟的工作流程相比，这种工作流程的速度快了20倍到100倍，并产生了更具生物学意义的结果。总而言之，MetaboAnalystR 3.0提供了一个高效的管道来支持开源R环境中的高通量全球代谢组学。
Liquid chromatography coupled to high-resolution mass spectrometry platforms are increasingly employed to comprehensively measure metabolome changes in systems biology and complex diseases. Over the past decade, several powerful computational pipelines have been developed for spectral processing, annotation, and analysis. However, significant obstacles remain with regard to parameter settings, computational efficiencies, batch effects, and functional interpretations. Here, we introduce MetaboAnalystR 3.0, a significantly improved pipeline with three key new features: (1) efficient parameter optimization for peak picking; (2) automated batch effect correction; and (3) more accurate pathway activity prediction. Our benchmark studies showed that this workflow was 20 similar to 100x faster compared to other well-established workflows and produced more biologically meaningful results. In summary, MetaboAnalystR 3.0 offers an efficient pipeline to support high-throughput global metabolomics in the open-source R environment.